The game's story mode is divided into three courses that follow the adventure about Amitie, a spunky girl who attends a magic school, where she is taught by Accord how to cast magical spells using Puyo. In the main story of the game, Accord has lost her Flying Cane, the equivalent of a magic wand, and claims to have a reward for the student who can find it. The player plays the role of Amitie as she ventures across the Puyo Puyo Fever world to find the cane, while meeting many wacky characters along the way and battling them. In a harder version of the story mode, one plays as Amitie's rival, Raffina. Which story mode one is playing determines what characters one will meet and which ultimately finds the wand. When playing as Raffina near to the end of the game, it is revealed that Accord never actually lost her flying cane. She then plans on revealing Accord's and Popoi's secret, but fails in her ending, as she is knocked unconscious by Accord, losing all memories of the flying cane incident. She regains consciousness near her school where Amitie and her friends congratulate her.